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HSEMB Conference and GenBank Release 168.0

Events of particular note this week¬†–¬†

The¬†HSEMB Conference –

The 26th Annual Houston Conference on Biomedical
Engineering Research (
http://www.hsemb.org) on 19-20 March 2009 at the University of Houston Hilton Hotel and Convention Center.

HSEMB has established the John Halter Award for Professional Achievement in Bioinformatics and Computational Biology.   The late Dr. John Halter is the founder of LifeFormulae, LLC.  http://www.lifeformulae.com/pages/about_jah_memorial.aspx is the link to our memorial to John.

Super Computing 2008

SC08 - Super Computing 2008, the International Conference for High
Performance Computing, Networking, Storage and Analysis. November
15-21, Austin Convention Center, Austin, Texas.
http://sc08.supercomputing.org/

And GenBank Release 168.0. –

Genbank Release 168.- flat files require roughtly 3871 GB for the sequence files only or 396 GB if you include the ’short directory’, ‘index’ and the *.txt files.¬† The ASN.1 data files require approximately 338 GB.

Recent statistics for non-WGS (Whole Genome Sequence), non-CON (Contig)  sequences are given below.

  Release  Date       Base Pairs   Entries

  167      Aug 2008   95033791652  92748599
  168      Oct 2008   97381682336  96400790

Recent statistics for WGS sequences:

  Release  Date       Base Pairs   Entries

  167      Aug 2008  118593509342  40214247
  168      Oct 2008  136085973423  46108952
 

During the 69 days between the close dates for GenBank Releases 167.0
and 168.0, the non-WGS/non-CON portion of GenBank grew by 2,347,890,684 basepairs and by 3,652,191 sequence records.

During that same period,1,111,311 records were updated. An average of about 69,036 non-WGS/non-CON records were added and/or updated per day.

Between releases 167.0 and 168.0, the WGS component of GenBank grew by 17,492,464,081 basepairs and by 5,894,705 records.

The combined WGS/non-WGS single-release increase of 19.84 Gbp for
Release 168.0 is the largest that GenBank has experienced, to date.
 

That’s a lot data. It’s a long, long way from the set of CDs that came out 4 times a year back in the late 90’s. Somewhere there are drawers and drawers of old Entrez CDs!¬† (Entrez is the engine used to search NCBI Life Sciences data.)

GenBank is considered an archive of information about sequences.  The nine-digit GI number, once the unique sequence identifier, have been supplanted by the Accession Number.

Speaking of NCBI data, we now have the complete set of the human (Homo Sapiens) data from NCBI’s dbSNP available through our LARTS product.¬† Currently, the files are not searchable by keyword, or keyword/element path.¬† This capability should be available to you the early part of next week.

Which brings me to the question.  Is GenBank data as important today as it was, say, 5 years ago?  If not GenBank, what NCBI data is considered critical to your current research and bioinformatics methods, and, if I might also ask, what are you doing with it?

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